Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate Synpcc7942_B2664 Synpcc7942_B2664 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__SynE:Synpcc7942_B2664 Length = 329 Score = 205 bits (521), Expect = 1e-57 Identities = 118/309 (38%), Positives = 171/309 (55%), Gaps = 22/309 (7%) Query: 8 ETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGSTII 67 +TIG TPLVR+N + + AK+EG NP SVK RI MI AE G L PG +I Sbjct: 13 QTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLLGPGKELI 72 Query: 68 EATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGAIRK 127 E TSGNTGI LA + +G + + M E +S+ERRK++ A+GA+++LT+ G GA+R+ Sbjct: 73 EPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKGMTGAVRR 132 Query: 128 VAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLMGVG 187 ++ +P +Y QF N N H +TT EIW T G + V+ VGT GT+ GV Sbjct: 133 AEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTGGTITGVS 192 Query: 188 KNLREK----------NPEIKIIEAQPTKG-------HYIQGLKSMEEAIVPAIYQADKI 230 + +++ PE + +Q G H IQG+ + +P + Sbjct: 193 RYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGA---GFIPENLDLSLV 249 Query: 231 DEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG--VIVVLFADRGE 288 D+ + +EEA A AR + +EG+ G+S GAA+ AA +LA++ + IVV+ D GE Sbjct: 250 DQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTIVVVLPDSGE 309 Query: 289 KYLSTKLFD 297 +YLST LFD Sbjct: 310 RYLSTALFD 318 Lambda K H 0.315 0.133 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 315 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 299 Length of database: 329 Length adjustment: 27 Effective length of query: 272 Effective length of database: 302 Effective search space: 82144 Effective search space used: 82144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory